3nyq - Revision history

OCA at 10:02, 14 February 2024

OCA — Wed, 14 Feb 2024 10:02:14 GMT

←Older revision		Revision as of 10:02, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='3nyq' size='340' side='right'caption='[[3nyq]], [[Resolution\|resolution]] 1.43Å' scene=''>		<StructureSection load='3nyq' size='340' side='right'caption='[[3nyq]], [[Resolution\|resolution]] 1.43Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3nyq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"actinomyces_coelicolor"_(muller_1908)_lieske_1921 "actinomyces~~ coelicolor~~" (muller 1908) lieske 1921~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NYQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NYQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3nyq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_coelicolor Streptomyces coelicolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NYQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NYQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MCA:METHYLMALONYL-COENZYME+A'>MCA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>~~</td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.43Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ite\|3ite]], [[3e7w\|3e7w]], [[1t5d\|1t5d]], [[2d1r\|2d1r]], [[1ry2\|1ry2]], [[1pg3\|1pg3]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MCA:METHYLMALONYL-COENZYME+A'>MCA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MatB, SCC24.15, SCO2444 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1902 "Actinomyces coelicolor" (Muller 1908) Lieske 1921])</td></tr>	+
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3nyq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nyq OCA], [https://pdbe.org/3nyq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nyq RCSB], [https://www.ebi.ac.uk/pdbsum/3nyq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nyq ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3nyq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nyq OCA], [https://pdbe.org/3nyq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nyq RCSB], [https://www.ebi.ac.uk/pdbsum/3nyq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nyq ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q9L0A2_STRCO Q9L0A2_STRCO]
-	In vitro experiments with modular polyketide synthases (PKSs) are often limited by the availability of polyketide extender units. To determine the polyketide extender units that can be biocatalytically accessed via promiscuous malonyl-CoA ligases, structural and functional studies were conducted on Streptomyces coelicolor MatB. We demonstrate that this adenylate-forming enzyme is capable of producing most CoA-linked polyketide extender units as well as pantetheine- and N-acetylcysteamine-linked analogs useful for in vitro PKS studies. Two ternary product complex structures, one containing malonyl-CoA and AMP and the other containing (2R)-methylmalonyl-CoA and AMP, were solved to 1.45 A and 1.43 A resolution, respectively. MatB crystallized in the thioester-forming conformation, making extensive interactions with the bound extender unit products. This first structural characterization of an adenylate-forming enzyme that activates diacids reveals the molecular details for how malonate and its derivatives are accepted. The orientation of the alpha-methyl group of bound (2R)-methylmalonyl-CoA, indicates that it is necessary to epimerize alpha-substituted extender units formed by MatB before they can be accepted by PKS acyltransferase domains. We demonstrate the in vitro incorporation of methylmalonyl groups ligated by MatB to CoA, pantetheine, or N-acetylcysteamine into a triketide pyrone by the terminal module of the 6-deoxyerythronolide B synthase. Additionally, a means for quantitatively monitoring certain in vitro PKS reactions using MatB is presented.	+
-		+
-	~~Enzymatic extender unit generation for in vitro polyketide synthase reactions~~: ~~structural and functional showcasing of Streptomyces coelicolor MatB.,Hughes AJ, Keatinge-Clay A Chem Biol. 2011 Feb 25;18(2):165-76. PMID:21338915<ref>PMID:21338915<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®~~/~~PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 3nyq" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Hughes, A J~~]]	+	[[Category: Streptomyces coelicolor]]
-	[[Category: ~~Keatinge-Clay, A T~~]]	+	[[Category: Hughes AJ]]
-	[[Category: ~~A/b topology ababa sandwich beta~~-~~barrel adenylate-forming enzyme fold]]~~	+	[[Category: Keatinge-Clay AT]]
-	~~[[Category: Ligase~~]]	+

OCA at 07:12, 12 May 2022

OCA — Thu, 12 May 2022 07:12:01 GMT

←Older revision		Revision as of 07:12, 12 May 2022
Line 1:		Line 1:

	==Malonyl-CoA Ligase Ternary Product Complex with Methylmalonyl-CoA and AMP bound==		==Malonyl-CoA Ligase Ternary Product Complex with Methylmalonyl-CoA and AMP bound==
-	<StructureSection load='3nyq' size='340' side='right' caption='[[3nyq]], [[Resolution\|resolution]] 1.43Å' scene=''>	+	<StructureSection load='3nyq' size='340' side='right'caption='[[3nyq]], [[Resolution\|resolution]] 1.43Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3nyq]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"actinomyces_coelicolor"_(muller_1908)_lieske_1921 "actinomyces coelicolor" (muller 1908) lieske 1921]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NYQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3NYQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3nyq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"actinomyces_coelicolor"_(muller_1908)_lieske_1921 "actinomyces coelicolor" (muller 1908) lieske 1921]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NYQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NYQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MCA:METHYLMALONYL-COENZYME+A'>MCA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MCA:METHYLMALONYL-COENZYME+A'>MCA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ite\|3ite]], [[3e7w\|3e7w]], [[1t5d\|1t5d]], [[2d1r\|2d1r]], [[1ry2\|1ry2]], [[1pg3\|1pg3]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ite\|3ite]], [[3e7w\|3e7w]], [[1t5d\|1t5d]], [[2d1r\|2d1r]], [[1ry2\|1ry2]], [[1pg3\|1pg3]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MatB, SCC24.15, SCO2444 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1902 "Actinomyces coelicolor" (Muller 1908) Lieske 1921])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MatB, SCC24.15, SCO2444 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1902 "Actinomyces coelicolor" (Muller 1908) Lieske 1921])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3nyq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nyq OCA], [~~http~~://pdbe.org/3nyq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3nyq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3nyq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3nyq ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3nyq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nyq OCA], [https://pdbe.org/3nyq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nyq RCSB], [https://www.ebi.ac.uk/pdbsum/3nyq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nyq ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Hughes, A J]]		[[Category: Hughes, A J]]
	[[Category: Keatinge-Clay, A T]]		[[Category: Keatinge-Clay, A T]]
	[[Category: A/b topology ababa sandwich beta-barrel adenylate-forming enzyme fold]]		[[Category: A/b topology ababa sandwich beta-barrel adenylate-forming enzyme fold]]
	[[Category: Ligase]]		[[Category: Ligase]]

OCA at 16:38, 4 August 2016

OCA — Thu, 04 Aug 2016 16:38:18 GMT

←Older revision		Revision as of 16:38, 4 August 2016
Line 1:		Line 1:
		+
	==Malonyl-CoA Ligase Ternary Product Complex with Methylmalonyl-CoA and AMP bound==		==Malonyl-CoA Ligase Ternary Product Complex with Methylmalonyl-CoA and AMP bound==
	<StructureSection load='3nyq' size='340' side='right' caption='[[3nyq]], [[Resolution\|resolution]] 1.43Å' scene=''>		<StructureSection load='3nyq' size='340' side='right' caption='[[3nyq]], [[Resolution\|resolution]] 1.43Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3nyq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Streptomyces_coelicolor Streptomyces~~ coelicolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NYQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NYQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3nyq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"actinomyces_coelicolor"_(muller_1908)_lieske_1921 "actinomyces coelicolor" (muller 1908) lieske 1921]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NYQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NYQ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MCA:METHYLMALONYL-COENZYME+A'>MCA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MCA:METHYLMALONYL-COENZYME+A'>MCA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ite\|3ite]], [[3e7w\|3e7w]], [[1t5d\|1t5d]], [[2d1r\|2d1r]], [[1ry2\|1ry2]], [[1pg3\|1pg3]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ite\|3ite]], [[3e7w\|3e7w]], [[1t5d\|1t5d]], [[2d1r\|2d1r]], [[1ry2\|1ry2]], [[1pg3\|1pg3]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MatB, SCC24.15, SCO2444 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1902 ~~Streptomyces~~ coelicolor])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MatB, SCC24.15, SCO2444 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1902 "Actinomyces coelicolor" (Muller 1908) Lieske 1921])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3nyq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nyq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3nyq RCSB], [http://www.ebi.ac.uk/pdbsum/3nyq PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3nyq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nyq OCA], [http://pdbe.org/3nyq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3nyq RCSB], [http://www.ebi.ac.uk/pdbsum/3nyq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3nyq ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3nyq" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Streptomyces coelicolor]]
	[[Category: Hughes, A J]]		[[Category: Hughes, A J]]
	[[Category: Keatinge-Clay, A T]]		[[Category: Keatinge-Clay, A T]]
	[[Category: A/b topology ababa sandwich beta-barrel adenylate-forming enzyme fold]]		[[Category: A/b topology ababa sandwich beta-barrel adenylate-forming enzyme fold]]
	[[Category: Ligase]]		[[Category: Ligase]]

OCA at 23:18, 3 January 2015

OCA — Sat, 03 Jan 2015 23:18:11 GMT

←Older revision		Revision as of 23:18, 3 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3nyq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_coelicolor Streptomyces coelicolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NYQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NYQ FirstGlance]. <br>		<table><tr><td colspan='2'>[[3nyq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_coelicolor Streptomyces coelicolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NYQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NYQ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MCA:METHYLMALONYL-COENZYME+A'>MCA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MCA:METHYLMALONYL-COENZYME+A'>MCA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ite\|3ite]], [[3e7w\|3e7w]], [[1t5d\|1t5d]], [[2d1r\|2d1r]], [[1ry2\|1ry2]], [[1pg3\|1pg3]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ite\|3ite]], [[3e7w\|3e7w]], [[1t5d\|1t5d]], [[2d1r\|2d1r]], [[1ry2\|1ry2]], [[1pg3\|1pg3]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MatB, SCC24.15, SCO2444 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1902 Streptomyces coelicolor])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MatB, SCC24.15, SCO2444 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1902 Streptomyces coelicolor])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3nyq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nyq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3nyq RCSB], [http://www.ebi.ac.uk/pdbsum/3nyq PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3nyq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nyq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3nyq RCSB], [http://www.ebi.ac.uk/pdbsum/3nyq PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 14:		Line 14:
	Enzymatic extender unit generation for in vitro polyketide synthase reactions: structural and functional showcasing of Streptomyces coelicolor MatB.,Hughes AJ, Keatinge-Clay A Chem Biol. 2011 Feb 25;18(2):165-76. PMID:21338915<ref>PMID:21338915</ref>		Enzymatic extender unit generation for in vitro polyketide synthase reactions: structural and functional showcasing of Streptomyces coelicolor MatB.,Hughes AJ, Keatinge-Clay A Chem Biol. 2011 Feb 25;18(2):165-76. PMID:21338915<ref>PMID:21338915</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, a database of the U.S. National Library of Medicine.<br>	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
	== References ==		== References ==
Line 21:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Streptomyces coelicolor]]		[[Category: Streptomyces coelicolor]]
-	[[Category: Hughes, A J.]]	+	[[Category: Hughes, A J]]
-	[[Category: Keatinge-Clay, A T.]]	+	[[Category: Keatinge-Clay, A T]]
	[[Category: A/b topology ababa sandwich beta-barrel adenylate-forming enzyme fold]]		[[Category: A/b topology ababa sandwich beta-barrel adenylate-forming enzyme fold]]
	[[Category: Ligase]]		[[Category: Ligase]]

OCA at 10:37, 28 May 2014

OCA — Wed, 28 May 2014 10:37:31 GMT

←Older revision		Revision as of 10:37, 28 May 2014
Line 1:		Line 1:
-	[[~~Image:~~3nyq.~~jpg~~\|~~left~~\|~~200px~~]]	+	==Malonyl-CoA Ligase Ternary Product Complex with Methylmalonyl-CoA and AMP bound==
		+	<StructureSection load='3nyq' size='340' side='right' caption='[[3nyq]], [[Resolution\|resolution]] 1.43Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3nyq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_coelicolor Streptomyces coelicolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NYQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NYQ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MCA:METHYLMALONYL-COENZYME+A'>MCA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ite\|3ite]], [[3e7w\|3e7w]], [[1t5d\|1t5d]], [[2d1r\|2d1r]], [[1ry2\|1ry2]], [[1pg3\|1pg3]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MatB, SCC24.15, SCO2444 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1902 Streptomyces coelicolor])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3nyq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nyq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3nyq RCSB], [http://www.ebi.ac.uk/pdbsum/3nyq PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In vitro experiments with modular polyketide synthases (PKSs) are often limited by the availability of polyketide extender units. To determine the polyketide extender units that can be biocatalytically accessed via promiscuous malonyl-CoA ligases, structural and functional studies were conducted on Streptomyces coelicolor MatB. We demonstrate that this adenylate-forming enzyme is capable of producing most CoA-linked polyketide extender units as well as pantetheine- and N-acetylcysteamine-linked analogs useful for in vitro PKS studies. Two ternary product complex structures, one containing malonyl-CoA and AMP and the other containing (2R)-methylmalonyl-CoA and AMP, were solved to 1.45 A and 1.43 A resolution, respectively. MatB crystallized in the thioester-forming conformation, making extensive interactions with the bound extender unit products. This first structural characterization of an adenylate-forming enzyme that activates diacids reveals the molecular details for how malonate and its derivatives are accepted. The orientation of the alpha-methyl group of bound (2R)-methylmalonyl-CoA, indicates that it is necessary to epimerize alpha-substituted extender units formed by MatB before they can be accepted by PKS acyltransferase domains. We demonstrate the in vitro incorporation of methylmalonyl groups ligated by MatB to CoA, pantetheine, or N-acetylcysteamine into a triketide pyrone by the terminal module of the 6-deoxyerythronolide B synthase. Additionally, a means for quantitatively monitoring certain in vitro PKS reactions using MatB is presented.

-	~~<!--~~	+	Enzymatic extender unit generation for in vitro polyketide synthase reactions: structural and functional showcasing of Streptomyces coelicolor MatB.,Hughes AJ, Keatinge-Clay A Chem Biol. 2011 Feb 25;18(2):165-76. PMID:21338915<ref>PMID:21338915</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3nyq"~~, ~~creates the "Structure Box" on the page~~.	+
-	~~You may change the PDB parameter~~ (~~which sets the PDB file loaded into the applet~~)	+
-	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~	+
-	~~or leave the SCENE parameter empty for the default display~~.	+
-	-->	+
-	~~{{STRUCTURE_3nyq\| PDB=3nyq \| SCENE= }}~~	+

-	~~===Malonyl-CoA Ligase Ternary Product Complex with Methylmalonyl-CoA and AMP bound===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph~~, ~~{{ABSTRACT_PUBMED_21338915}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 21338915 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_21338915}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3nyq]] is a 1 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Streptomyces_coelicolor Streptomyces coelicolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NYQ OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:21338915<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Streptomyces coelicolor]]		[[Category: Streptomyces coelicolor]]
	[[Category: Hughes, A J.]]		[[Category: Hughes, A J.]]
	[[Category: Keatinge-Clay, A T.]]		[[Category: Keatinge-Clay, A T.]]
		+	[[Category: A/b topology ababa sandwich beta-barrel adenylate-forming enzyme fold]]
		+	[[Category: Ligase]]

OCA: Protected "3nyq" [edit=sysop:move=sysop]

OCA — Wed, 30 Mar 2011 08:06:33 GMT

Protected "3nyq" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:06, 30 March 2011

OCA at 08:06, 30 March 2011

OCA — Wed, 30 Mar 2011 08:06:28 GMT

←Older revision		Revision as of 08:06, 30 March 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3nyq.jpg\|left\|200px]]

-	The ~~entry 3nyq~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3nyq", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3nyq\| PDB=3nyq \| SCENE= }}

-	~~Authors: Hughes, A.J., Keatinge~~-~~Clay, A.T.~~	+	===Malonyl-CoA Ligase Ternary Product Complex with Methylmalonyl-CoA and AMP bound===

-	Description: Malonyl-CoA Ligase Ternary Product Complex with Methylmalonyl-CoA and AMP bound

-	~~''Page seeded by~~ [http://oca.weizmann.ac.il/oca OCA ] ~~on Wed Jul 28 12~~:26:~~45 2010''~~	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21338915}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21338915 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21338915}}
		+
		+	==About this Structure==
		+	[[3nyq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_coelicolor Streptomyces coelicolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NYQ OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:21338915</ref><references group="xtra"/>
		+	[[Category: Streptomyces coelicolor]]
		+	[[Category: Hughes, A J.]]
		+	[[Category: Keatinge-Clay, A T.]]

OCA: New page: '''Unreleased structure''' The entry 3nyq is ON HOLD Authors: Hughes, A.J., Keatinge-Clay, A.T. Description: Malonyl-CoA Ligase Ternary Product Complex with Methylmalonyl-CoA and AMP b...

OCA — Wed, 28 Jul 2010 08:20:02 GMT

New page: '''Unreleased structure''' The entry 3nyq is ON HOLD Authors: Hughes, A.J., Keatinge-Clay, A.T. Description: Malonyl-CoA Ligase Ternary Product Complex with Methylmalonyl-CoA and AMP b...

New page

'''Unreleased structure'''

The entry 3nyq is ON HOLD

Authors: Hughes, A.J., Keatinge-Clay, A.T.

Description: Malonyl-CoA Ligase Ternary Product Complex with Methylmalonyl-CoA and AMP bound

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 28 12:26:45 2010''